After the success of the Super Mini Mario World theme park, Mario and Pauline open an expansion of it. A crowd of Toads are in line for the opening celebration, along with Donkey Kong. As Donkey Kong reaches the front of the line, he discovers the tickets have just sold out. Donkey Kong bursts into anger and grabs Pauline. As Donkey Kong runs for the elevator, Mario leaps to rescue Pauline, but ends up failing and ripping the fringe of her dress. As Mario lies on the ground, a few Mini Marios come towards him, volunteering to help save Pauline.

Later on, when Mario reaches to the top of the tower, he finds Pauline is there waiting for him. Relieved, Mario opens the door, ready to hug her, but then all of a sudden, Donkey Kong turns off the light and captures Pauline once again. Mario and the Mini Marios jump out of the tower after Donkey Kong, leading them to more floors.

After all the trouble, Mario once again opens the door and sees Donkey Kong, Pauline, and two Mini Marios. Confused by this, Mario then sees Pauline with a clipboard, showing that the Mini Mario model passed the test. Mario shrugs, and then celebrates with Donkey Kong, Pauline, and the rest of his Minis.

Mario vs. Donkey Kong: Minis March Again! features a less detailed story with slight changes from March of the Minis. The game also lacks some of the functions the Minis use, like jumping and changing directions. Instead, the minis move by themselves after being activated, while the player changes the obstacles around to lead the minis to the goal. Also, every mini must be in the goal near the same amount of time; otherwise, the door will close, locking out some of the minis. Lives are also new in Minis March Again!; the player will lose a life if time runs out, if a Mini Mario dies, or if the door closes before all the minis have reached it. Plus Mode is also available after beating the first four worlds, unlike March of the Minis, which did not have the mode. Both games share the Construction Zone function, but Minis March Again! doesn't contain as many items as March of the Minis.

In this game, there are three different type of Minis that the player can use in levels, and are used to move around within the worlds. These include Mini Mario, Mini Toad, and Mini Peach. Though there are no significant differences between the types of Minis, the player must have to save different minis at different times in the game.

Each floor of The Super Mini-Mario World Theme Park, excluding the basement and the rooftop, is diverse and has its own unique elements that sets it apart. They each consist of seven levels, a key level, a DK boss battle, and a special level.

Thanks to the runaway success of Super Mini Mario World, Mario and Pauline have expanded their toy-filled theme park and invited everyone to the opening celebration. Everyone, that is, except Donkey Kong, who was too late to get in! Donkey Kong decides to crash the party and kidnaps Pauline along the way! Can Mario and his Mini Marios rescue Pauline from Donkey Kong’s clutches yet again?

In addition, make sure to explore the Construction Zone, where you’ll find all the tools needed to make your own original levels. You can then share your masterpieces or download levels created by others via Nintendo Wi-Fi Connection and broadband Internet access, or via local wireless.

The re-opening of Mario’s theme park, Super Mini Mario World, was going so well... until Donkey Kong burst in and kidnapped the hapless Pauline once again! So it’s up to you and the Mini Marios – tiny mechanical Mario toys – to rescue Pauline from that crazed ape’s clutches.

Instead of controlling the Mini Marios directly, you use the stylus to manipulate objects in each trap-laden level, and lead the fragile toys safely to the exit. Once you clear all eight levels on a floor, you’ll get a chance to pummel Donkey Kong with your Mini Mario-launching cannon!

Another feature is the Construction Zone, which allows you to create your own original levels, play levels that you or others have made, and share or download levels via Nintendo Wi-Fi Connection or local wireless communications.

This game was one of few downloadable games that were on sale via Club Nintendo, at 150 coins, until January 10, 2012. However, even though this game is a DSiWare downloadable title, a Nintendo 3DS is required. This game was also included as one of the Elite Status gifts in 2012, available to Gold and Platinum members. It was since become available again on Sept. 3rd 2013, until Oct. 6th 2013. Once again it is 150 coins.